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(-) Description

Title :  CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE NANA (TIGR4) IN COMPLEX WITH DANA
 
Authors :  H. Gut, G. Xu, G. L. Taylor, M. A. Walsh
Date :  18 Feb 11  (Deposition) - 27 Apr 11  (Release) - 08 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Sialidase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Gut, G. Xu, G. L. Taylor, M. A. Walsh
Structural Basis For Streptococcus Pneumoniae Nana Inhibition By Influenza Antivirals Zanamivir And Oseltamivir Carboxylate.
J. Mol. Biol. V. 409 496 2011
PubMed-ID: 21514303  |  Reference-DOI: 10.1016/J.JMB.2011.04.016

(-) Compounds

Molecule 1 - NEURAMINIDASE A
    ChainsA, B
    EC Number3.2.1.18
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    FragmentCATALYTIC DOMAIN, RESIDUES 280-754
    Organism ScientificSTREPTOCOCCUS PNEUMONIAE
    Organism Taxid170187
    Other DetailsTHE SEQUENCE NUMBERING ABOVE CORRESPONDS TO THE CLOSEST UNIPROT SEQUENCE MATCH UNP B2DJD9. THE SEQUENCE NUMBERING FOR THE ENTRY SHOULD BE 303-777
    StrainTIGR4
    SynonymNANA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2DAN2Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
3FMT5Ligand/IonFORMIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DAN1Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
3FMT3Ligand/IonFORMIC ACID
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DAN1Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
3FMT2Ligand/IonFORMIC ACID

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:332 , ILE A:333 , ARG A:351 , ASP A:357 , ILE A:401 , ASP A:402 , ASP A:419 , ILE A:427 , PHE A:428 , TYR A:575 , LEU A:583 , GLN A:587 , ARG A:648 , ARG A:706 , TYR A:737 , HOH A:2295 , HOH A:2296 , HOH A:2297 , HOH A:2298BINDING SITE FOR RESIDUE DAN A1777
2AC2SOFTWAREARG B:332 , ILE B:333 , ARG B:351 , ASP B:357 , ASP B:402 , ASP B:419 , ILE B:427 , PHE B:428 , TYR B:575 , GLN B:587 , ARG B:648 , ARG B:706 , TYR B:737 , HOH B:2282 , HOH B:2283 , HOH B:2284BINDING SITE FOR RESIDUE DAN B1777
3AC3SOFTWARESER A:526 , ASP A:527 , ASP A:528 , THR A:532BINDING SITE FOR RESIDUE FMT A1778
4AC4SOFTWAREASN A:502 , LYS A:509 , THR A:510 , SER A:511BINDING SITE FOR RESIDUE CL A1779
5AC5SOFTWAREGLY B:501 , ASN B:502 , LYS B:509 , THR B:510 , SER B:511BINDING SITE FOR RESIDUE CL B1778
6AC6SOFTWAREPRO A:541 , LYS A:544 , ALA A:545 , HOH A:2168BINDING SITE FOR RESIDUE FMT A1780
7AC7SOFTWARETYR B:525 , SER B:526 , ASP B:527 , ASP B:528 , THR B:532 , SER B:534 , HOH B:2285BINDING SITE FOR RESIDUE FMT B1779
8AC8SOFTWAREHIS B:566 , ARG B:569 , GLU B:717 , ASN B:719 , HOH B:2190BINDING SITE FOR RESIDUE FMT B1780
9AC9SOFTWAREGLN A:741 , HOH A:2286 , HOH A:2300BINDING SITE FOR RESIDUE FMT A1781

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YA6)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Glu A:691 -Gly A:692
2Gly A:703 -Pro A:704
3Ala A:761 -Tyr A:762
4Gly B:703 -Pro B:704
5Ala B:761 -Tyr B:762

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YA6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YA6)

(-) Exons   (0, 0)

(no "Exon" information available for 2YA6)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:470
 aligned with NANA_STREE | P62575 from UniProtKB/Swiss-Prot  Length:1035

    Alignment length:470
                                   331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791
           NANA_STREE   322 ALTEKTDIFESGRNGKPNKDGIKSYRIPALLKTDKGTLIAGADERRLHSSDWGDIGMVIRRSEDNGKTWGDRVTITNLRDNPKASDPSIGSPVNIDMVLVQDPETKRIFSIYDMFPEGKGIFGMSSQKEEAYKKIDGKTYQILYREGEKGAYTIRENGTVYTPDGKATDYRVVVDPVKPAYSDKGDLYKGNQLLGNIYFTTNKTSPFRIAKDSYLWMSYSDDDGKTWSAPQDITPMVKADWMKFLGVGPGTGIVLRNGPHKGRILIPVYTTNNVSHLNGSQSSRIIYSDDHGKTWHAGEAVNDNRQVDGQKIHSSTMNNRRAQNTESTVVQLNNGDVKLFMRGLTGDLQVATSKDGGVTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEYIILSNAGGPKRENGMVHLARVEENGELTWLKHNPIQKGEFAYNSLQELGNGEYGILYEHTEKGQNAYTLSFRKFNWDFLSK 791
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..............eeeeeeeee.....eeeeeeee.........eeeeeeee..........eeee.........hhhhh..eeeeeeeee......eeeeeeee...hhhhhh.......eeee..eeeeeeee......eee....eee.....eeeeee.....hhhhh...eeee..eeeee..........eee....eeeeeee..........eehhhhhh...eeeeee..ee.ee.........eeeeeeeee..hhhhhh.eeeeeee.......ee.......eee..eee......hhhhh...eeeee.....eeeee.....eeeeeee...........eeeeeee......eeeeeee..eeeeeeeee.....eeeeeeeeee.....eeeeeeeeeeeee...eeeeeee..eeeeeeee........eeeeeeeehhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ya6 A 307 ALTEKTDIFESGRNGNPNKDGIKSYRIPALLKTDKGTLIAGADERRLHSSDWGDIGMVIRRSEDNGKTWGDRVTITNLRDNPKASDPSIGSPVNIDMVLVQDPETKRIFSIYDMFPEGKGIFGMSSQKEEAYKKIDGKTYQILYREGEKGAYTIRENGTVYTPDGKATDYRVVVDPVKPAYSDKGDLYKGDQLLGNIYFTTNKTSPFRIAKDSYLWMSYSDDDGKTWSAPQDITPMVKADWMKFLGVGPGTGIVLRNGPHKGRILIPVYTTNNVSHLDGSQSSRVIYSDDHGKTWHAGEAVNDNRQVDGQKIHSSTMNNRRAQNTESTVVQLNNGDVKLFMRGLTGDLQVATSKDGGVTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEYIILSNAGGPKRENGMVHLARVEENGELTWLKHNPIQKGEFAYNSLQELGNGEYGILYEHTEKGQNAYTLSFRKFNWEFLSK 776
                                   316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776

Chain B from PDB  Type:PROTEIN  Length:470
 aligned with NANA_STREE | P62575 from UniProtKB/Swiss-Prot  Length:1035

    Alignment length:470
                                   331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791
           NANA_STREE   322 ALTEKTDIFESGRNGKPNKDGIKSYRIPALLKTDKGTLIAGADERRLHSSDWGDIGMVIRRSEDNGKTWGDRVTITNLRDNPKASDPSIGSPVNIDMVLVQDPETKRIFSIYDMFPEGKGIFGMSSQKEEAYKKIDGKTYQILYREGEKGAYTIRENGTVYTPDGKATDYRVVVDPVKPAYSDKGDLYKGNQLLGNIYFTTNKTSPFRIAKDSYLWMSYSDDDGKTWSAPQDITPMVKADWMKFLGVGPGTGIVLRNGPHKGRILIPVYTTNNVSHLNGSQSSRIIYSDDHGKTWHAGEAVNDNRQVDGQKIHSSTMNNRRAQNTESTVVQLNNGDVKLFMRGLTGDLQVATSKDGGVTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEYIILSNAGGPKRENGMVHLARVEENGELTWLKHNPIQKGEFAYNSLQELGNGEYGILYEHTEKGQNAYTLSFRKFNWDFLSK 791
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..............eeeeeeeee.....eeeeeeee.........eeeeeeee..........eeee.........hhhhh..eeeeeeeee......eeeeeeee...hhhhh........eeee..eeeeeeee.....eeee....eee.....eeeeee.....hhhhh...eeee..eeeee..........ee.....eeeeeee..........eehhhhhh......eee..ee.ee.........eeeeeee....hhhhhh.eeeeeee.......ee.......eee..eee......hhhhh...eeeee.....eeeee.....eeeeeee...........eeeeeee......eeeeeee..eeeeeeeee.....eeeeeeeeee.....eeeeeeeeeeeee...eeeee....eeeeeeee........eeeeeeeehhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ya6 B 307 ALTEKTDIFESGRNGNPNKDGIKSYRIPALLKTDKGTLIAGADERRLHSSDWGDIGMVIRRSEDNGKTWGDRVTITNLRDNPKASDPSIGSPVNIDMVLVQDPETKRIFSIYDMFPEGKGIFGMSSQKEEAYKKIDGKTYQILYREGEKGAYTIRENGTVYTPDGKATDYRVVVDPVKPAYSDKGDLYKGDQLLGNIYFTTNKTSPFRIAKDSYLWMSYSDDDGKTWSAPQDITPMVKADWMKFLGVGPGTGIVLRNGPHKGRILIPVYTTNNVSHLDGSQSSRVIYSDDHGKTWHAGEAVNDNRQVDGQKIHSSTMNNRRAQNTESTVVQLNNGDVKLFMRGLTGDLQVATSKDGGVTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEYIILSNAGGPKRENGMVHLARVEENGELTWLKHNPIQKGEFAYNSLQELGNGEYGILYEHTEKGQNAYTLSFRKFNWEFLSK 776
                                   316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2YA6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YA6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YA6)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NANA_STREE | P62575)
molecular function
    GO:0052794    exo-alpha-(2->3)-sialidase activity    Catalysis of the hydrolysis of alpha-(2->3)-glycosidic linkages of terminal sialic residues in substrates.
    GO:0052795    exo-alpha-(2->6)-sialidase activity    Catalysis of the hydrolysis of alpha-(2->6)-glycosidic linkages of terminal sialic residues in substrates.
    GO:0052796    exo-alpha-(2->8)-sialidase activity    Catalysis of the hydrolysis of alpha-(2->8)-glycosidic linkages of terminal sialic residues in substrates.
    GO:0004308    exo-alpha-sialidase activity    Catalysis of the hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)-glycosidic linkages of terminal sialic residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NANA_STREE | P625752vvz 2ya4 2ya5 2ya7 2ya8 4c1x 4zxk 5kky

(-) Related Entries Specified in the PDB File

2ya4 CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE NANA (TIGR4 )
2ya5 CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE NANA (TIGR4 ) IN COMPLEX WITH SIALIC ACID
2ya7 CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE NANA (TIGR4 ) IN COMPLEX WITH ZANAMIVIR
2ya8 CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE NANA (TIGR4 ) IN COMPLEX WITH OSELTAMIVIR CARBOXYLATE